diff -u -r1.5 -r1.6
--- ImageMapperII.java	13 Apr 2011 09:31:01 -0000	1.5
+++ ImageMapperII.java	21 Apr 2011 20:45:43 -0000	1.6
@@ -20,6 +20,8 @@

 public class ImageMapperII {
 	
 	private static final int INTERESTING_CUT = 1;

+	private static final int PIX_WIDEN = 2;
+	

 	
 	private static final double pixWidth = 45.0;
 	private static final double pixHeight = 33.0;

@@ -52,7 +54,10 @@

 	private int dPrint;
 	String outFolderBroken;
 	

-	public ImageMapperII(String imageFile, String outFile, int debugFlag) throws IOException{

+	private int sideNum;
+	
+	public ImageMapperII(int side, String imageFile, String outFile, int debugFlag) throws IOException{
+		sideNum = side;

 		dPrint = 0;
 		doLowRes = false;
 		outFolderBroken = "/Users/maxinion/Documents/Work/CDMS/imagingII/out2-28/broken/";

@@ -118,8 +123,8 @@

 	}
 	
 	//alternative longer constructor, with full debugbroken stuff

-	public ImageMapperII(String imageFile, String outFile, int debugFlag, int printBroken, String outBroken) throws IOException{
-		this(imageFile, outFile, debugFlag);

+	public ImageMapperII(int side, String imageFile, String outFile, int debugFlag, int printBroken, String outBroken) throws IOException{
+		this(side, imageFile, outFile, debugFlag);

 		dPrint = printBroken;
 		outFolderBroken = outBroken;
 	}

@@ -163,25 +168,37 @@

 		// return the coordinates of the subimage we take as we grid
 		// normally just a box of size defined by the 620x460 camera pixel grid
 		// sometimes, at the edges, have to define subimages only up to the edges

-		int[] out = new int[2];

+		int[] out = new int[4];
+		out[0] = (int) pixWidth*i;
+		out[1] = (int) pixHeight*j;

 		
 		if(i < nPixWidth-1 && j < nPixHeight -1){ // normal areas

-			out[0] = (int) pixWidth;
-			out[1] = (int) pixHeight;

+			out[2] = (int) pixWidth;
+			out[3] = (int) pixHeight;

 		}
 		else if(i < nPixWidth -1 && j == nPixHeight -1){ // at the bottom

-			out[0] = (int) pixWidth;
-			out[1] = (int) (imageHeight - pixHeight*j);

+			out[2] = (int) pixWidth;
+			out[3] = (int) (imageHeight - pixHeight*j);

 		}
 		else if(i == nPixWidth-1 && j < nPixHeight -1){// at the right

-			out[0] = (int) (imageWidth - pixWidth*i);
-			out[1] = (int) pixHeight;

+			out[2] = (int) (imageWidth - pixWidth*i);
+			out[3] = (int) pixHeight;

 		}
 		else{ // at the bottom right
 			if(debug==1) System.out.println("At the bottom right: should only be here once. i = " + i +" j = " + j);

-			out[0] = (int) (imageWidth - pixWidth*i);
-			out[1] = (int) (imageHeight - pixHeight*j);

+			out[2] = (int) (imageWidth - pixWidth*i);
+			out[3] = (int) (imageHeight - pixHeight*j);
+		}
+		
+		if(i!=0 && i!= nPixWidth-1){ // in the left-right middle, not along the edge
+			out[0] = out[0] - PIX_WIDEN; //if(debug==1) System.out.println("widen i=" + i);
+			out[2] = out[2] + 2 * PIX_WIDEN;
+		}
+		if(j!=0 && j!=nPixHeight-1){ // in the top-bottom middle, not along the edge
+			out[1] = out[1] - PIX_WIDEN; //if(debug==1) System.out.println("widen j=" + j);
+			out[3] = out[3] + 2 * PIX_WIDEN;

 		}

+		

 		return out;
 	}
 	

@@ -190,8 +207,8 @@

 		for(int i = 0; i < nPixWidth; i++){
 			for(int j =0; j < nPixHeight; j++){
 				int[] boxCoords = getSubCoords(i,j);

-				BufferedImage sub = image.getSubimage((int) pixWidth*i, (int) pixHeight*j,
-						boxCoords[0], boxCoords[1]);

+				BufferedImage sub = image.getSubimage(boxCoords[0], boxCoords[1],
+						boxCoords[2], boxCoords[3]);

 				
 				if(isInteresting(sub))
 					flag[i][j] = true;

@@ -207,7 +224,8 @@

         	output.write("BEGIN_RUN\n");
         	output.write("MM\n");
         	output.write("SET_DATUM\n");

-        	output.write("c:\\Partrtn\\IZipDatum_PeaceSide1_x2_5.RTN\n");

+        	if(sideNum == 1) output.write("c:\\Partrtn\\IZipDatum_PeaceSide1_x2_5.RTN\n");
+        	else if(sideNum == 2) output.write("c:\\Partrtn\\IZipDatum_PeaceSide2_x2_5.RTN\n");

         }
 		
 	    //loop over flag list; if set to true, then output

@@ -236,7 +254,7 @@

 		fmt1.format("%.6f", coord[0]);
 		fmt2.format("%.6f", coord[1]); 
 

-		if(debug==0) output.write("c:\\Partrtn\\IZipOriginTakePicture_x2_5.RTN,"+fmt1+","+fmt2+",0,0,0,0\n");

+		if(debug==0) output.write("c:\\Partrtn\\IZipOriginTakePicture_x690.RTN,"+fmt1+","+fmt2+",0,0,0,0\n");

 		else if(debug==1) output.write(fmt1+","+fmt2+"\n");
 	}
 	

diff -u -r1.5 -r1.6
--- ImageMapperIIRun.java	13 Apr 2011 09:31:01 -0000	1.5
+++ ImageMapperIIRun.java	21 Apr 2011 20:45:43 -0000	1.6
@@ -10,11 +10,11 @@

 	public static void main(String[] args) {
 
 		try {

-			ImageMapperII mapper = new ImageMapperII("/Users/maxinion/Documents/Work/CDMS/imagingII/qets-hires1.png",
-					"/Users/maxinion/Documents/Work/CDMS/imagingII/out4-11/qets1-out.txt",0);

+			ImageMapperII mapper = new ImageMapperII(1,"/Users/maxinion/Documents/Work/CDMS/imagingII/qets-hires-charge1.png",
+					"/Users/maxinion/Documents/Work/CDMS/imagingII/out4-21/qets1-charge-out.txt",0);

 			mapper.enableLowRes("/Users/maxinion/Documents/Work/CDMS/imagingII/OGP_scansettings_6Apr11_x177.txt");
 			mapper.doAll();

-			//mapper.roughStitch("/Users/maxinion/Desktop/MaxScanTestL09FullII/MaxScanTestL09FullII-","/Users/maxinion/Desktop/stitched.png");

+			//mapper.roughStitch("/Users/maxinion/Desktop/IZipTestWaferBatch28_L13_Side2/IZipTestWaferBatch28_L13_Side2HR-","/Users/maxinion/Desktop/stitched-charge-2.png");

 		} catch (IOException e) {
 			e.printStackTrace();
 		}